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From Peter Klügl <peter.klu...@averbis.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Tue, 03 Nov 2015 15:10:51 GMT
Yes, I will do that.

Who else plans to provide patches for it? Just to avoid duplicate work
and to coordnate the efforts ...

Is there a development dataset which was utilized for the initial
development, and if yes, is it possible to contribute it too?

My first step would be:
- set up a maven project
- set up a development pipeline in a test (with cTAKES components
replacing the previous ANNIE preprocessing)

Best,

Peter

Am 02.11.2015 um 18:04 schrieb Pei Chen:
> Hi Peter/Azad,
> Per INFRA-10579, since there is only a limited history, they suggested
> we do the export/import ourselves.
> The initial code base has been imported into:
> sandbox/ctakes-clinical-deid
>
> Feel free to do an svn co
> https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/
> and attach any patches to CTAKES-384 until you have commit access...
>
> --Pei
>
>
> On Mon, Nov 2, 2015 at 3:56 AM, Peter Klügl <peter.kluegl@averbis.com> wrote:
>> Hi,
>>
>> I just wanted to ask about the current status. I assume that the source
>> is not yet in svn, right? Let me know when I can do something (in case I
>> miss some mail on this list).
>>
>> Best,
>>
>> Peter
>>
>> Am 13.10.2015 um 21:17 schrieb Pei Chen:
>>> Thanks Azad.
>>> I submitted a Jira to infra to help us do the import (that way we will try
>>> and preserve the commit history).
>>> In the meantime, would you mind filling out the ICLA[1].
>>>
>>> [Reminder: Let's keep it in sandbox and not release it until all of the 3rd
>>> party dependencies licenses have been verified.]
>>>
>>> [1] http://www.apache.org/licenses/#clas
>>>
>>> Thanks,
>>> Pei
>>>
>>>     Pei Chen
>>> Wired Informatics <http://www.wiredinformatics.com>
>>> 265 Franklin St Ste 1702
>>> Boston, MA 02110
>>> tel: (617) 433-7544
>>> Pei.Chen@wiredinformatics.com
>>>
>>> On Sun, Oct 11, 2015 at 3:51 PM, Azad Dehghan <azad.dehghan@gmail.com>
>>> wrote:
>>>
>>>> 1: Yes. Sorted.
>>>> 3: Code attached to the Jira.
>>>>
>>>> Azad
>>>>
>>>> On 8 October 2015 at 20:03, Chen, Pei <Pei.Chen@childrens.harvard.edu>
>>>> wrote:
>>>>
>>>>> This is great news!
>>>>>> What is the current status and procedure? Is there an explicit
>>>>> contribution to cTAKES? Is there an ICLA? What about the license of the
>>>>> sourceforge project?
>>>>> Jira has been opened to track this:
>>>>> https://issues.apache.org/jira/browse/CTAKES-384
>>>>>
>>>>> 1) Azad, would you be willing to switch licenses?  I believe it's
>>>>> currently GNU3 -> ASL 2.0?
>>>>> 2) Create a project/module in cTAKES sandbox for this
>>>>> 3) Export/Import sourceforge and attach the code to the Jira initially.
>>>>> One of the current cTAKES committers can commit it to the repo (Until
>>>> folks
>>>>> can commit directly to the ctakes repo directly going forward.)
>>>>>
>>>>> -----Original Message-----
>>>>> From: Peter Klügl [mailto:peter.kluegl@averbis.com]
>>>>> Sent: Thursday, October 08, 2015 8:06 AM
>>>>> To: dev@ctakes.apache.org
>>>>> Subject: Re: Combining Knowledge- and Data-driven Methods for
>>>>> De-identification of Clinical Narratives
>>>>>
>>>>> Hi,
>>>>>
>>>>> I can offer my help here if required.
>>>>>
>>>>> I have experience in translating JAPE rules to UIMA Ruta and already
>>>>> worked with clinical notes, e.g., also concerning deidentification.
>>>>>
>>>>> The problem is that I can only invest a few hours in the next two weeks.
>>>>> I will have more time next month or even more next year.
>>>>>
>>>>> What is the current status and procedure? Is there an explicit
>>>>> contribution to cTAKES? Is there an ICLA? What about the license of the
>>>>> sourceforge project?
>>>>>
>>>>> Best,
>>>>>
>>>>> Peter
>>>>>
>>>>> Am 01.10.2015 um 16:20 schrieb Pei Chen:
>>>>>> Hi Azad,
>>>>>> This is awesome news.  Thanks for adding in the code that was
>>>>>> referenced by the paper.  I'll create a Jira to track we need to
port
>>>>>> it over to UIMA/Ruta.
>>>>>>
>>>>>> In the meantime, the link is at:
>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p_
>>>>>>
>>>> clinical-2Ddeid_code_ci_master_tree_&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=yjhqco4EH0XrR798kbkzfYcFQ8z8MR9UF8mMRSjKTH0&s=_k7AbwzkVrRwTrNC3LArZ5hQ5Q47eh06KCDla7UBugY&e=
>>>>> for those who may be interested in helping out...
>>>>>> --Pei
>>>>>>
>>>>>> Hello Pei,
>>>>>>
>>>>>> I hope all is well.
>>>>>>
>>>>>> I have now uploaded the source code for cDeid
>>>>>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p
>>>>>> _clinical-2Ddeid_code_ci_master_tree_&d=BQICaQ&c=qS4goWBT7poplM69zy_3x
>>>>>> hKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m
>>>>>>
>>>> =yjhqco4EH0XrR798kbkzfYcFQ8z8MR9UF8mMRSjKTH0&s=_k7AbwzkVrRwTrNC3LArZ5hQ5Q47eh06KCDla7UBugY&e=
>>>>> ) ; I have tried to make the code as portable and modular as possible
>>>> with
>>>>> some trade-off for performance. This should help with porting the code
to
>>>>> cTAKES/UIMA.
>>>>>> Once you let the community know I will try to get involved to help
>>>>>> with translating JAPE to RUTA, etc.
>>>>>>
>>>>>> Best,
>>>>>> Azad


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